Author: scooter
Date: 2012-04-05 12:39:09 -0700 (Thu, 05 Apr 2012)
New Revision: 28743
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyEdge.java
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNode.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyEdge.java
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyNode.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
core3/impl/trunk/ding-impl/graph-render/src/main/java/org/cytoscape/graph/render/stateful/GraphRenderer.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
core3/impl/trunk/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapperTask.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
Log:
Changes to remove getIndex from the model API and replace it with calls to
getSUID
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyEdge.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyEdge.java
2012-04-05 01:29:35 UTC (rev 28742)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyEdge.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -81,17 +81,7 @@
ANY;
}
-
/**
- * An index of this edge within this network. The index is guaranteed
to
- * be between 0 and (the number of edges in the network) - 1. This index
- * can be used as a parameter to {@link CyNetwork#getEdge}, however it
is not
- * necessarily an index into {@link CyNetwork#getEdgeList}.
- * @return An index for this edge within this network.
- */
- long getIndex();
-
- /**
* Returns the source node determining this edge. It will never be null.
* For undirected networks this method will consistently
* return the same node.
Modified:
core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNode.java
===================================================================
--- core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNode.java
2012-04-05 01:29:35 UTC (rev 28742)
+++ core3/api/trunk/model-api/src/main/java/org/cytoscape/model/CyNode.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -38,17 +38,7 @@
* @CyAPI.Api.Interface
*/
public interface CyNode extends CyIdentifiable {
-
/**
- * An index of this node within this network. The index is guaranteed
to
- * be between 0 and (the number of nodes in the network) - 1. This index
- * can be used as a parameter to {@link CyNetwork#getNode}, however it
is not
- * necessarily an index into {@link CyNetwork#getNodeList}.
- * @return An index for this node within this network.
- */
- long getIndex();
-
- /**
* Returns the network referenced by this node. If no
* network has been specified this method will return null.
*
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyEdgeTest.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -62,8 +62,8 @@
@Test
public void testGetIndex() {
- assertTrue("edge index >= 0", eDir.getIndex() >= 0);
- assertTrue("edge index >= 0", eUndir.getIndex() >= 0);
+ assertTrue("edge index >= 0", eDir.getSUID() >= 0);
+ assertTrue("edge index >= 0", eUndir.getSUID() >= 0);
}
@Test
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNetworkTest.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -44,7 +44,7 @@
public void testAddNode() {
CyNode n = net.addNode();
assertNotNull("node is not null", n);
- assertTrue("node index >= 0", n.getIndex() >= 0);
+ assertTrue("node index >= 0", n.getSUID() >= 0);
// Doesn't make sense for subnetworks
//assertTrue("node index < num node", n.getIndex() <
net.getNodeCount());
@@ -130,14 +130,14 @@
// add a directed edge
CyEdge e1 = net.addEdge(n1, n2, true);
assertNotNull("edge is not null", e1);
- assertTrue("edge index >= 0", e1.getIndex() >= 0);
+ assertTrue("edge index >= 0", e1.getSUID() >= 0);
//assertTrue("edge index < num edge", e1.getIndex() <
net.getEdgeCount());
assertEquals("edge count", 1, net.getEdgeCount());
// add an undirected edge
CyEdge e2 = net.addEdge(n2, n3, false);
assertNotNull("edge is not null", e2);
- assertTrue("edge index >= 0", e2.getIndex() >= 0);
+ assertTrue("edge index >= 0", e2.getSUID() >= 0);
//assertTrue("edge index < num edge", e2.getIndex() <
net.getEdgeCount());
assertEquals("edge count", 2, net.getEdgeCount());
@@ -803,9 +803,9 @@
CyNode n2 = net.addNode();
CyNode n3 = net.addNode();
- assertEquals("nodes are equivalent", n1,
net.getNode(n1.getIndex()));
- assertEquals("nodes are equivalent", n2,
net.getNode(n2.getIndex()));
- assertEquals("nodes are equivalent", n3,
net.getNode(n3.getIndex()));
+ assertEquals("nodes are equivalent", n1,
net.getNode(n1.getSUID()));
+ assertEquals("nodes are equivalent", n2,
net.getNode(n2.getSUID()));
+ assertEquals("nodes are equivalent", n3,
net.getNode(n3.getSUID()));
// test random index
assertNull("node is null ", net.getNode(72));
@@ -826,8 +826,8 @@
CyEdge e1 = net.addEdge(n1, n2, true);
CyEdge e2 = net.addEdge(n2, n3, true);
- assertEquals("edges are equivalent", e1,
net.getEdge(e1.getIndex()));
- assertEquals("edges are equivalent", e2,
net.getEdge(e2.getIndex()));
+ assertEquals("edges are equivalent", e1,
net.getEdge(e1.getSUID()));
+ assertEquals("edges are equivalent", e2,
net.getEdge(e2.getSUID()));
// test random index
assertNull("edge is null ", net.getEdge(72));
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/AbstractCyNodeTest.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -55,8 +55,8 @@
public void testGetIndex() {
CyNode n1 = net.addNode();
CyNode n2 = net.addNode();
- assertTrue("index >= 0", n1.getIndex() >= 0);
- assertTrue("index >= 0", n2.getIndex() >= 0);
+ assertTrue("index >= 0", n1.getSUID() >= 0);
+ assertTrue("index >= 0", n2.getSUID() >= 0);
}
@Test
@@ -114,10 +114,10 @@
assertEquals(0,net.getNodeCount());
CyNode n0 = net.addNode();
CyNode n1 = net.addNode();
- long n0i = n0.getIndex();
- long n1i = n1.getIndex();
+ long n0i = n0.getSUID();
+ long n1i = n1.getSUID();
net.removeNodes(Collections.singletonList(n0));
- long nnli = n1.getIndex();
+ long nnli = n1.getSUID();
assertEquals(nnli,n1i);
}
@@ -126,8 +126,8 @@
assertEquals(0,net.getNodeCount());
CyNode n0 = net.addNode();
CyNode n1 = net.addNode();
- long n0i = n0.getIndex();
- long n1i = n1.getIndex();
+ long n0i = n0.getSUID();
+ long n1i = n1.getSUID();
assertEquals(net.getNode(n0i),n0);
assertEquals(net.getNode(n1i),n1);
assertTrue( net.removeNodes(Collections.singletonList(n0)) );
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyEdge.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyEdge.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyEdge.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -50,10 +50,6 @@
index = ind;
}
- public long getIndex() {
- return getSUID().longValue();
- }
-
public CyNode getSource() {
return source;
}
Modified:
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyNode.java
===================================================================
---
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyNode.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/api/trunk/model-api/src/test/java/org/cytoscape/model/DummyCyNode.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -49,10 +49,6 @@
nested = null;
}
- public long getIndex() {
- return getSUID().longValue();
- }
-
public List<CyNode> getNeighborList(CyEdge.Type edgeType) {
return new ArrayList<CyNode>();
}
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DEdgeDetails.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -823,8 +823,8 @@
final CyNetwork graph = m_view.m_drawPersp;
- final long srcNodeIndex =
edgeView.getModel().getSource().getIndex();
- final long trgNodeIndex =
edgeView.getModel().getTarget().getIndex();
+ final long srcNodeIndex =
edgeView.getModel().getSource().getSUID();
+ final long trgNodeIndex =
edgeView.getModel().getTarget().getSUID();
// Calculate anchors necessary for self edges.
if (srcNodeIndex == trgNodeIndex) {
@@ -843,9 +843,9 @@
for(final CyEdge selfEdge: selfEdgeList) {
// while (selfEdges.hasNext()) {
// final int e2 = selfEdges.nextInt();
- final long e2 = selfEdge.getIndex();
+ final long e2 = selfEdge.getSUID();
- if (e2 == edge.getIndex())
+ if (e2 == edge.getSUID())
break;
if (((EdgeAnchors)
m_view.getDEdgeView(e2)).numAnchors() == 0)
@@ -893,7 +893,7 @@
for(final CyEdge conEdge: conEdgeList) {
// while (conEdges.hasNext()) {
// m_heap.toss(conEdges.nextInt());
- m_heap.toss(conEdge.getIndex());
+ m_heap.toss(conEdge.getSUID());
}
final LongEnumerator otherEdges =
m_heap.orderedElements(false);
@@ -902,7 +902,7 @@
// If the first other edge is the same as this edge,
// (i.e. we're at the end of the list?).
- if (otherEdge == edge.getIndex())
+ if (otherEdge == edge.getSUID())
break;
// So we don't count the other edge twice?
@@ -910,7 +910,7 @@
// Count the number of other edges.
while (true) {
- if (edge.getIndex() == (otherEdge =
otherEdges.nextLong()))
+ if (edge.getSUID() == (otherEdge =
otherEdges.nextLong()))
break;
if (((EdgeAnchors)
m_view.getDEdgeView(otherEdge)).numAnchors() == 0)
@@ -1009,7 +1009,7 @@
if (lineType(edge) == DEdgeView.STRAIGHT_LINES)
anchorInx = anchorInx / 2;
- if (m_view.m_selectedAnchors.count((edge.getIndex() << 6) |
anchorInx) > 0)
+ if (m_view.m_selectedAnchors.count((edge.getSUID() << 6) |
anchorInx) > 0)
return m_view.getAnchorSelectedPaint();
else
return m_view.getAnchorUnselectedPaint();
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/DGraphView.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -808,7 +808,7 @@
* Should synchronize around m_lock.
*/
private DNodeView addNodeViewInternal(final CyNode node) {
- final long nodeInx = node.getIndex();
+ final long nodeInx = node.getSUID();
final NodeView oldView = m_nodeViewMap.get(node);
if (oldView != null)
@@ -841,7 +841,7 @@
throw new NullPointerException("edge is null");
synchronized (m_lock) {
- final long edgeInx = edge.getIndex();
+ final long edgeInx = edge.getSUID();
final EdgeView oldView = m_edgeViewMap.get(edge);
if (oldView != null)
@@ -910,7 +910,7 @@
* @return The NodeView object that was removed.
*/
public NodeView removeNodeView(CyNode node) {
- return removeNodeView(node.getIndex());
+ return removeNodeView(node.getSUID());
}
/**
@@ -992,7 +992,7 @@
* @return The EdgeView that was removed.
*/
public EdgeView removeEdgeView(CyEdge edge) {
- return removeEdgeView(edge.getIndex());
+ return removeEdgeView(edge.getSUID());
}
/**
@@ -1649,11 +1649,11 @@
CyEdge currEdge = model.getEdge(edge);
CyNode source = currEdge.getSource();
- long sourceId = source.getIndex();
+ long sourceId = source.getSUID();
nodeIds.put(sourceId);
CyNode target = currEdge.getTarget();
- long targetId = target.getIndex();
+ long targetId = target.getSUID();
nodeIds.put(targetId);
}
@@ -2201,7 +2201,7 @@
public List<NodeView> getNodeViewsList() {
ArrayList<NodeView> list = new
ArrayList<NodeView>(getNodeViewCount());
for (CyNode nn : getNetwork().getNodeList())
- list.add(getDNodeView(nn.getIndex()));
+ list.add(getDNodeView(nn.getSUID()));
return list;
}
@@ -2602,13 +2602,13 @@
@Override
public View<CyNode> getNodeView(final CyNode node) {
- return (View<CyNode>) getDNodeView(node.getIndex());
+ return (View<CyNode>) getDNodeView(node.getSUID());
}
@Override
public View<CyEdge> getEdgeView(final CyEdge edge) {
- return (View<CyEdge>) getDEdgeView(edge.getIndex());
+ return (View<CyEdge>) getDEdgeView(edge.getSUID());
}
@@ -2681,4 +2681,4 @@
public String getRenderingEngineID() {
return ENGINE_ID;
}
-}
\ No newline at end of file
+}
Modified:
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
===================================================================
---
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/ding-impl/ding-presentation-impl/src/main/java/org/cytoscape/ding/impl/InnerCanvas.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -684,8 +684,8 @@
final Iterable<CyEdge> touchingEdges =
graph.getAdjacentEdgeIterable(nodeObj, CyEdge.Type.ANY);
for ( CyEdge e : touchingEdges ) {
- final long edge = e.getIndex();
- final long otherNode = node ^
e.getSource().getIndex() ^ e.getTarget().getIndex();
+ final long edge = e.getSUID();
+ final long otherNode = node ^
e.getSource().getSUID().longValue() ^ e.getTarget().getSUID().longValue();
if (m_hash.get(otherNode) < 0) {
m_view.m_spacial.exists(otherNode, m_view.m_extentsBuff, 0);
@@ -715,7 +715,7 @@
for ( CyEdge edge : touchingEdges ) {
// final int edge = e.getIndex(); //
Positive.
final double segThicknessDiv2 =
m_view.m_edgeDetails.segmentThickness(edge) / 2.0d;
- final long otherNode = node ^
edge.getSource().getIndex() ^ edge.getTarget().getIndex();
+ final long otherNode = node ^
edge.getSource().getSUID().longValue() ^ edge.getTarget().getSUID().longValue();
final CyNode otherNodeObj =
graph.getNode(otherNode);
if (m_hash.get(otherNode) < 0) {
@@ -727,7 +727,7 @@
final float[] srcExtents;
final float[] trgExtents;
- if (node ==
edge.getSource().getIndex()) {
+ if (node ==
edge.getSource().getSUID().longValue()) {
srcShape = nodeShape;
trgShape =
otherNodeShape;
srcExtents =
m_view.m_extentsBuff;
@@ -777,7 +777,7 @@
if (m_path2.intersects(xMin -
segThicknessDiv2, yMin - segThicknessDiv2,
(xMax -
xMin) + (segThicknessDiv2 * 2),
(yMax -
yMin) + (segThicknessDiv2 * 2)))
-
stack.push(edge.getIndex());
+
stack.push(edge.getSUID().longValue());
}
}
Modified:
core3/impl/trunk/ding-impl/graph-render/src/main/java/org/cytoscape/graph/render/stateful/GraphRenderer.java
===================================================================
---
core3/impl/trunk/ding-impl/graph-render/src/main/java/org/cytoscape/graph/render/stateful/GraphRenderer.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/ding-impl/graph-render/src/main/java/org/cytoscape/graph/render/stateful/GraphRenderer.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -239,8 +239,8 @@
final Iterable<CyEdge> touchingEdges =
graph.getAdjacentEdgeIterable(graph.getNode(node),CyEdge.Type.ANY);
for ( CyEdge e : touchingEdges ) {
- final long edge = e.getIndex();
- final long otherNode = node ^
e.getSource().getIndex() ^ e.getTarget().getIndex();
+ final long edge = e.getSUID();
+ final long otherNode = node ^
e.getSource().getSUID() ^ e.getTarget().getSUID();
if (nodeBuff.get(otherNode) < 0)
runningEdgeCount++;
@@ -329,7 +329,7 @@
Iterable<CyEdge> touchingEdges =
graph.getAdjacentEdgeIterable(graph.getNode(node),CyEdge.Type.ANY);
for ( CyEdge edge : touchingEdges ) {
- final long otherNode = node ^
edge.getSource().getIndex() ^ edge.getTarget().getIndex();
+ final long otherNode = node ^
edge.getSource().getSUID() ^ edge.getTarget().getSUID();
if (nodeBuff.get(otherNode) <
0) { // Has not yet been rendered.
nodePositions.exists(otherNode, floatBuff2, 0);
@@ -351,8 +351,8 @@
final byte nodeShape =
nodeDetails.shape(cyNode);
Iterable<CyEdge> touchingEdges =
graph.getAdjacentEdgeIterable(cyNode,CyEdge.Type.ANY);
for ( CyEdge edge : touchingEdges ) {
- final long otherNode = node ^
edge.getSource().getIndex()
- ^
edge.getTarget().getIndex();
+ final long otherNode = node ^
edge.getSource().getSUID()
+ ^
edge.getTarget().getSUID();
final CyNode otherCyNode =
graph.getNode(otherNode);
if (nodeBuff.get(otherNode) <
0) { // Has not yet been rendered.
@@ -369,7 +369,7 @@
final byte trgShape;
final float[]
srcExtents;
final float[]
trgExtents;
- if (node ==
edge.getSource().getIndex()) {
+ if (node ==
edge.getSource().getSUID()) {
srcShape =
nodeShape;
trgShape =
otherNodeShape;
srcExtents =
floatBuff1;
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/gml/GMLNetworkReader.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -268,7 +268,7 @@
nodeIDMap.put(label, node);
gml_id2order.put(nodes.get(idx), idx);
- node_root_index_pairs.get(idx).value =
Long.valueOf(node.getIndex());
+ node_root_index_pairs.get(idx).value =
node.getSUID();
} else {
throw new RuntimeException("GML id " +
nodes.get(idx) + " has a duplicated label: " + label);
}
@@ -310,7 +310,7 @@
network.getRow(edge).set("interaction", label);
edge_names.add(idx, edge);
- edge_root_index_pairs.get(idx).value =
Long.valueOf(edge.getIndex());
+ edge_root_index_pairs.get(idx).value =
edge.getSUID();
} else {
throw new RuntimeException("Non-existant
source/target node for edge with gml (source,target): " +
sources.get(idx) + "," + targets.get(idx));
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/read/xgmml/handler/ReadDataManager.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -473,8 +473,8 @@
CyNetwork net = getCurrentNetwork();
// But first get the actual source/target instances from the
current network,
// because both node instances have to belong to the same root
or sub-network.
- CyNode actualSrc = net.getNode(source.getIndex());
- CyNode actualTgt = net.getNode(target.getIndex());
+ CyNode actualSrc = net.getNode(source.getSUID());
+ CyNode actualTgt = net.getNode(target.getSUID());
if (getDocumentVersion() < 3.0 || !isSessionFormat()) {
if (actualSrc == null || actualTgt == null) {
@@ -488,10 +488,10 @@
net = getRootNetwork();
if (actualSrc == null)
- actualSrc =
net.getNode(source.getIndex());
+ actualSrc =
net.getNode(source.getSUID());
if (actualTgt == null)
- actualTgt =
net.getNode(target.getIndex());
+ actualTgt =
net.getNode(target.getSUID());
}
}
Modified:
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
===================================================================
---
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/io-impl/impl/src/main/java/org/cytoscape/io/internal/util/ReadCache.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -107,10 +107,10 @@
if (xgmmlId != null) {
if (element instanceof CyNode) {
nodeByIdMap.put(xgmmlId, (CyNode) element);
- index = ((CyNode) element).getIndex();
+ index = ((CyNode) element).getSUID();
} else if (element instanceof CyEdge) {
edgeByIdMap.put(xgmmlId, (CyEdge) element);
- index = ((CyEdge) element).getIndex();
+ index = ((CyEdge) element).getSUID();
} else if (element instanceof CyNetwork) {
networkByIdMap.put(xgmmlId, (CyNetwork)
element);
} else if (element instanceof CyNetworkView) {
Modified:
core3/impl/trunk/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapperTask.java
===================================================================
---
core3/impl/trunk/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapperTask.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/layout-jgraph-impl/src/main/java/csapps/layout/JGraphLayoutWrapperTask.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -129,7 +129,7 @@
if (canceled) return;
View<CyNode> node_view = networkView.getNodeView(n);
- DefaultGraphCell jcell = new
DefaultGraphCell(n.getIndex());
+ DefaultGraphCell jcell = new
DefaultGraphCell(n.getSUID());
// Set bounds
Rectangle2D bounds = new Rectangle2D.Double(
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyEdgeImpl.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -46,7 +46,6 @@
class CyEdgeImpl extends CyIdentifiableImpl implements CyEdge {
final private CyNode source;
final private CyNode target;
- // final private long index;
final private boolean directed;
CyEdgeImpl(long suid, CyNode src, CyNode tgt, boolean dir, long ind) {
@@ -54,16 +53,14 @@
source = src;
target = tgt;
directed = dir;
- // index = ind;
}
/**
* @see org.cytoscape.model.CyEdge#getIndex()
- */
- @Override
public long getIndex() {
return getSUID().longValue();
}
+ */
/**
* @see org.cytoscape.model.CyEdge#getSource()
@@ -98,8 +95,6 @@
sb.append(target.toString());
sb.append(" directed: ");
sb.append(Boolean.toString(directed));
- sb.append(" index: ");
- sb.append(Long.toString(getIndex()));
return sb.toString();
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/CyNodeImpl.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -39,24 +39,22 @@
class CyNodeImpl extends CyIdentifiableImpl implements CyNode {
- // final private long index;
private CyNetwork nestedNet;
final private CyEventHelper eventHelper;
CyNodeImpl(long suid, long ind, final CyEventHelper eventHelper) {
super(suid);
- // index = ind;
nestedNet = null;
this.eventHelper = eventHelper;
}
/**
* @see org.cytoscape.model.CyNode#getIndex()
- */
@Override
public long getIndex() {
return getSUID().longValue();
}
+ */
/**
* @see org.cytoscape.model.CyNode#getNetworkPointer()
@@ -89,6 +87,6 @@
@Override
public String toString() {
- return "Node suid: " + getSUID() + " index: " + getIndex();
+ return "Node suid: " + getSUID();
}
}
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/EdgePointer.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -52,7 +52,7 @@
target = t;
directed = dir;
cyEdge = edge;
- index = edge.getIndex();
+ index = edge.getSUID();
nextOutEdge = null;
prevOutEdge = null;
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/NodePointer.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -58,7 +58,7 @@
NodePointer(final CyNode cyn) {
cyNode = cyn;
- index = cyn.getIndex();
+ index = cyn.getSUID();
outDegree = 0;
inDegree = 0;
Modified:
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
===================================================================
---
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/model-impl/impl/src/main/java/org/cytoscape/model/internal/SimpleNetwork.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -222,7 +222,7 @@
return node;
NodePointer n = new NodePointer(node);
- nodePointers.put(node.getIndex(),n);
+ nodePointers.put(node.getSUID(),n);
nodeCount++;
firstNode = n.insert(firstNode);
}
@@ -242,7 +242,7 @@
// remove adjacent edges from network
removeEdgesInternal(getAdjacentEdgeList(n,
CyEdge.Type.ANY));
- final NodePointer node =
nodePointers.remove(n.getIndex());
+ final NodePointer node =
nodePointers.remove(n.getSUID());
firstNode = node.remove(firstNode);
nodeCount--;
@@ -274,7 +274,7 @@
e = new EdgePointer(source, target, directed, edge);
- edgePointers.put(edge.getIndex(),e);
+ edgePointers.put(edge.getSUID(),e);
edgeCount++;
}
@@ -291,7 +291,7 @@
if (!containsEdge(edge))
return false;
- final EdgePointer e =
edgePointers.remove(edge.getIndex());
+ final EdgePointer e =
edgePointers.remove(edge.getSUID());
e.remove();
@@ -309,7 +309,7 @@
final NodePointer thisNode;
synchronized (this) {
- thisNode = nodePointers.get(node.getIndex());
+ thisNode = nodePointers.get(node.getSUID());
}
if ( thisNode == null )
@@ -325,7 +325,7 @@
final EdgePointer thisEdge;
synchronized (this) {
- thisEdge = edgePointers.get(edge.getIndex());
+ thisEdge = edgePointers.get(edge.getSUID());
}
if ( thisEdge == null )
@@ -565,7 +565,7 @@
private NodePointer getNodePointer(final CyNode node) {
assert(node != null);
- return nodePointers.get(node.getIndex());
+ return nodePointers.get(node.getSUID());
}
Modified:
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
===================================================================
---
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/psi-mi-impl/impl/src/main/java/org/cytoscape/psi_mi/internal/cyto_mapper/MapToCytoscape.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -213,7 +213,7 @@
for (int i = 0; i < nodeList.size(); i++) {
CyNode node = nodeList.get(i);
- nodeIndices[i] = node.getIndex();
+ nodeIndices[i] = node.getSUID();
}
return nodeIndices;
@@ -229,7 +229,7 @@
for (int i = 0; i < edgeList.size(); i++) {
CyEdge edge = edgeList.get(i);
- edgeIndices[i] = edge.getIndex();
+ edgeIndices[i] = edge.getSUID();
}
return edgeIndices;
@@ -463,7 +463,7 @@
mapEdgeAttributes(interaction, edge, network);
- long edgeRootGraphIndex = edge.getIndex();
+ Long edgeRootGraphIndex = edge.getSUID();
@SuppressWarnings("unchecked")
List<Long> indexes = (List<Long>)
interaction.getAttribute(ROOT_GRAPH_INDEXES);
Modified:
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
===================================================================
---
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2012-04-05 01:29:35 UTC (rev 28742)
+++
core3/impl/trunk/search-impl/src/main/java/org/cytoscape/search/internal/EnhancedSearchIndex.java
2012-04-05 19:39:09 UTC (rev 28743)
@@ -75,13 +75,13 @@
this.taskMonitor.setProgress(0.1);
for (CyNode cyNode : nodeList) {
- writer.addDocument(createDocument(network,
cyNode, EnhancedSearch.NODE_TYPE, cyNode.getIndex()));
+ writer.addDocument(createDocument(network,
cyNode, EnhancedSearch.NODE_TYPE, cyNode.getSUID()));
}
this.taskMonitor.setProgress(0.6);
List<CyEdge> edgeList = network.getEdgeList();
for (CyEdge cyEdge : edgeList) {
- writer.addDocument(createDocument(network,
cyEdge, EnhancedSearch.EDGE_TYPE, cyEdge.getIndex()));
+ writer.addDocument(createDocument(network,
cyEdge, EnhancedSearch.EDGE_TYPE, cyEdge.getSUID()));
}
// Optimize and close the writer to finish building the
index
--
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